23 July, 2021

Background

Documentation

  • code (R, python, java, c++ etc)
  • reports, manuscripts, theses (pdf, docx, html etc)

    How do we keep these in sync?

Markdown

---
title: Example markdown
author: D. Author
date: 16-06-2020
---

This is the title
=====================

## Section 1

A paragraph of text containing a word that is **emphasised** or ~~strikethrough~~.
Followed by an unordered list: 

- item 1
- item 2

Or perhaps an enumerated list:

1. item 1
2. item 2

### Subsection 1.1

There might be a [link](https://www.markdownguide.org/) or even a table:

+-----------+---------+-----------------------+
| Item      | Example | Description           |
+===========+=========+=======================+
| numeric   | 12.34   | floating point number |
+-----------+---------+-----------------------+
| character | 'Site'  | words                 |
+-----------+---------+-----------------------+
| ...       |         |                       |
+-----------+---------+-----------------------+

Pandoc

Markdown - pandoc

---
title: Example markdown
author: D. Author
date: 16-06-2020
---

This is the title
=====================

## Section 1

A paragraph of text containing a word that is **emphasised** or ~~strikethrough~~.
Followed by an unordered list: 

- item 1
- item 2

Or perhaps an enumerated list:

1. item 1
2. item 2

### Subsection 1.1

There might be a [link](https://www.markdownguide.org/) or even a table:

+-----------+---------+-----------------------+
| Item      | Example | Description           |
+===========+=========+=======================+
| numeric   | 12.34   | floating point number |
+-----------+---------+-----------------------+
| character | 'Site'  | words                 |
+-----------+---------+-----------------------+
| ...       |         |                       |
+-----------+---------+-----------------------+

pdf

Markdown - pandoc

---
title: Example markdown
author: D. Author
date: 16-06-2020
---

This is the title
=====================

## Section 1

A paragraph of text containing a word that is **emphasised** or ~~strikethrough~~.
Followed by an unordered list: 

- item 1
- item 2

Or perhaps an enumerated list:

1. item 1
2. item 2

### Subsection 1.1

There might be a [link](https://www.markdownguide.org/) or even a table:

+-----------+---------+-----------------------+
| Item      | Example | Description           |
+===========+=========+=======================+
| numeric   | 12.34   | floating point number |
+-----------+---------+-----------------------+
| character | 'Site'  | words                 |
+-----------+---------+-----------------------+
| ...       |         |                       |
+-----------+---------+-----------------------+

html

Markdown - pandoc

---
title: Example markdown
author: D. Author
date: 16-06-2020
---

This is the title
=====================

## Section 1

A paragraph of text containing a word that is **emphasised** or ~~strikethrough~~.
Followed by an unordered list: 

- item 1
- item 2

Or perhaps an enumerated list:

1. item 1
2. item 2

### Subsection 1.1

There might be a [link](https://www.markdownguide.org/) or even a table:

+-----------+---------+-----------------------+
| Item      | Example | Description           |
+===========+=========+=======================+
| numeric   | 12.34   | floating point number |
+-----------+---------+-----------------------+
| character | 'Site'  | words                 |
+-----------+---------+-----------------------+
| ...       |         |                       |
+-----------+---------+-----------------------+

docx

Markdown - pandoc

Rmarkdown

---
title: Example markdown
author: D. Author
date: 16-06-2020
---

# This is the title

```{r summary, eval=TRUE, results='markup'}
x <- rnorm(10)
summary(x)
`` `

Rmarkdown - knitr

rmarkdown::render('file.Rmd', output_format='html_document')


Rmarkdown templates

plos

pnas

elsevier